BlockCounter.

What is BlockCounter?

BlockCounter analyses a FASTA formatted global alignment
(e.g. the output of DIALIGN 2) or LAGAN for the presence
of blocks of complete identity. The lengths of the blocks will lie within
a user-defined range. The program generates data in the
form of a frequency distribution (length of conserved
block versus frequency of conservation) and (optionally) a plot of
the positions of all specified block sizes in relation to a reference
sequence.

For example, if
the range of block sizes is between 10 and 20 nucleotides,
the data generated might look like:

Block size Frequency
10 33
11 30
12 26
.. ..
.. ..
20 7

The original BlockCounter script was designed by Dr. Mike Chapman.
Modifications were made by Dr. Ian Donaldson to create a plot of all the
block positions in relation to the reference sequence.
A second program by Dr. Mike Chapman, called Masker, is used to mask
specified features of the global alignment.
This script is also
available and may be used to mask any named GFF file feature.